#define EPI(x) (LIBUSB_ENDPOINT_IN | (unsigned char)(x))
#define EPO(x) (LIBUSB_ENDPOINT_OUT | (unsigned char)(x))
#ifdef WIN32
#define BITFORCE_TIMEOUT_MS 500
#define MODMINER_TIMEOUT_MS 200
#else
#define BITFORCE_TIMEOUT_MS 200
#define MODMINER_TIMEOUT_MS 100
#endif
#ifdef USE_BITFORCE
// N.B. transfer size is 512 with USB2.0, but only 64 with USB1.1
static struct usb_endpoints bfl_eps[] = {
{ LIBUSB_TRANSFER_TYPE_BULK, 64, EPI(1), 0 },
{ LIBUSB_TRANSFER_TYPE_BULK, 64, EPO(2), 0 }
};
#endif
#ifdef USE_MODMINER
static struct usb_endpoints mmq_eps[] = {
{ LIBUSB_TRANSFER_TYPE_BULK, 64, EPI(3), 0 },
{ LIBUSB_TRANSFER_TYPE_BULK, 64, EPO(3), 0 }
};
#endif
// TODO: Add support for (at least) Isochronous endpoints
static struct usb_find_devices find_dev[] = {
/*
#ifdef USE_ICARUS
void Plink::driverSCREEPI()
{
///////////////////////////////
// Gene-based epistasis
//////////////////////////////////////////
// Case-control samples only
affCoding(*this);
//////////////////////////////////////////
// SNP-major mode analysis
if (!par::SNP_major)
Ind2SNP();
//////////////////////////////////////////
// Requires that sets have been speciefied
if (par::set_test) readSet();
else error("Need to specify genes with --set {filename} when using --genepi\n");
//////////////////
// SET statistics
Set S(snpset);
//////////////////////////////////////////////
// Prune SET (0-sized sets, MAF==0 SNPs, etc)
S.pruneSets(*this);
int ns = snpset.size();
if (ns < 2)
error("Need to specify at least two fully valid sets\n");
int n = 0;
int ncase = 0;
/////////////////////////////////////////////////////////
// Prune based on VIF
string original_outfile = par::output_file_name;
// Case-control? Prune cases and controls together...
if (!par::epi_caseonly)
{
printLOG("\nConsidering cases and controls: ");
setFlags(false);
vector<Individual*>::iterator person = sample.begin();
while ( person != sample.end() )
{
if ( ! (*person)->missing )
{
(*person)->flag = true;
n++;
}
person++;
}
par::output_file_name += ".all";
S.pruneMC(*this,false,par::vif_threshold);
//S.pruneMC(*this,false,1000);
}
// Case-only? Prune cases only...
else
{
printLOG("\nConsidering cases: ");
setFlags(false);
vector<Individual*>::iterator person = sample.begin();
while ( person != sample.end() )
{
if ( (*person)->aff && ! (*person)->missing )
{
(*person)->flag = true;
ncase++;
}
person++;
n++;
}
par::output_file_name += ".case";
S.pruneMC(*this,false,par::vif_threshold);
//S.pruneMC(*this,false,1000);
}
par::output_file_name = original_outfile;
// Write finalized set
ofstream SET1, SET2;
string f = par::output_file_name + ".all.set.in";
printLOG("Writing combined pruned-in set file to [ " + f + " ]\n");
SET1.open(f.c_str(),ios::out);
f = par::output_file_name + ".all.set.out";
printLOG("Writing combined pruned-out set file to [ " + f + " ]\n");
SET2.open(f.c_str(),ios::out);
for (int s=0; s<snpset.size(); s++)
{
int nss = snpset[s].size();
SET1 << setname[s] << "\n";
SET2 << setname[s] << "\n";
for (int j=0; j<nss; j++)
{
if (S.cur[s][j])
SET1 << locus[snpset[s][j]]->name << "\n";
else
SET2 << locus[snpset[s][j]]->name << "\n";
}
SET1 << "END\n\n";
SET2 << "END\n\n";
}
SET1.close();
SET2.close();
// Prune empty sets once more:
S.pruneSets(*this);
ns = snpset.size();
if (ns < 2)
error("Need to specify at least two fully valid sets\n");
////////////////////////////////
// Set up permutation structure
// Specialized (i.e. cannot use Perm class) as this
// requires a block-locus permutation
// First block is fixed
vector<vector<int> > blperm(ns);
vector<vector<int> > blperm_case(ns);
vector<vector<int> > blperm_control(ns);
for (int i=0; i<ns; i++)
{
// A slot for each individual per locus
for (int j=0; j<n; j++)
if ( ! sample[j]->missing )
blperm[i].push_back(j);
// A slot for each individual per locus
for (int j=0; j<n; j++)
if ( ! sample[j]->missing && sample[j]->aff )
blperm_case[i].push_back(j);
// A slot for each individual per locus
for (int j=0; j<n; j++)
if ( ! sample[j]->missing && !sample[j]->aff )
blperm_control[i].push_back(j);
}
////////////////////////////////////////////
// Open file and print header for results
ofstream EPI(f.c_str(), ios::out);
EPI.open(f.c_str(), ios::out);
EPI.precision(4);
////////////////////////////////////////
// Analysis (calls genepi functions)
if (!par::epi_caseonly)
CCA_logit(false,blperm,S,*this);
else
CCA_caseonly(false,blperm_case,S,*this);
if (!par::permute)
return;
if (!par::silent)
cout << "\n";
} // End of screepi
